A Biallelic Variant of the RNA Exosome Gene, EXOSC4, Associated With Neurodevelopmental Defects Impairs RNA Exosome Function and Translation

Authors

Milo B Fasken
Sara W Leung
Lauryn A Cureton
Maha Al-Awadi
Adila Al-Kindy
Ambro van Hoof
Sohail Khoshnevis
Homa Ghalei
Almundher Al-Maawali
Anita H Corbett

Publication Date

8-1-2024

Journal

Journal of Biological Chemistry

Abstract

The RNA exosome is an evolutionarily conserved complex required for both precise RNA processing and decay. Pathogenic variants in EXOSC genes, which encode structural subunits of this complex, are linked to several autosomal recessive disorders. Here, we describe a missense allele of the EXOSC4 gene that causes a collection of clinical features in two affected siblings. This missense variant (NM_019037.3: exon3:c.560T>C) changes a leucine residue within a conserved region of EXOSC4 to proline (p.Leu187Pro). The two affected individuals show prenatal growth restriction, failure to thrive, global developmental delay, intracerebral and basal ganglia calcifications, and kidney failure. Homozygosity for the damaging variant was identified by exome sequencing with Sanger sequencing to confirm segregation. To explore the functional consequences of this amino acid change, we modeled EXOSC4-L187P in the corresponding budding yeast protein, Rrp41 (Rrp41-L187P). Cells that express Rrp41-L187P as the sole copy of the essential Rrp41 protein show growth defects. Steady-state levels of both Rrp41-L187P and EXOSC4-L187P are decreased compared to controls, and EXOSC4-L187P shows decreased copurification with other RNA exosome subunits. RNA exosome target transcripts accumulate in rrp41-L187P cells, including the 7S precursor of 5.8S rRNA. Polysome profiles show a decrease in actively translating ribosomes in rrp41-L187P cells as compared to control cells with the incorporation of 7S pre-rRNA into polysomes. This work adds EXOSC4 to the structural subunits of the RNA exosome that have been linked to human disease and defines foundational molecular defects that could contribute to the adverse phenotypes caused by EXOSC pathogenic variants.

Keywords

Humans, Protein Biosynthesis, Exosome Multienzyme Ribonuclease Complex, Mutation, Missense, Male, Female, Neurodevelopmental Disorders, RNA-Binding Proteins, Alleles, Exosomes, Saccharomyces cerevisiae, Saccharomyces cerevisiae Proteins

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Associated Data

PMID: 39009343